Kun:LabNotes/SingleCellExpr/2015-4-25

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Extract mapped reads from Bam files for IGV inspection[edit]

  • I wrote a script for quick extraction of mapped sequencing reads near a list of genes from multiple data sets. This makes it easy to visually inspect the mapped reads with IGV, checking whether the genes/exons of interest have read coverage or not.
 ./extract_bam_for_selected_genes.pl gene_list data_set_folder output_folder
   THREE ARGUMENTS:
     gene_list: a plain text file containing the HUGO IDs for a list of genes, one gene per line
     data_set_folder: the folder that contains multiple mapped data set, each data set folder has a suffix "_mapped"
     output_folder: the folder where all extracted bam files will be placed.
 Example:  in /home/kunzhang/temp/brain_bulk_bams, run
 /home/kunzhang/RNAseq/SCAP/scripts/extract_bam_for_selected_genes.pl brain_selected_genes.txt  \
   /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR . 
  • All the extracted bam files can be loaded into IGV for visual inspection.